Summary of the project: COver the past few years the new concept of dependence receptors has emerged in the field of tumorigenesis. These receptors have the ability to be active not only in presence of their ligands, inducing a "positive" signal of proliferation and cell survival, but also in the absence of the ligands. In this situation, dependence receptors are not inactive but they actively induce a "negative" signal of programmed cell death, or apoptosis. This ability allows these receptors to act as tumor suppressor genes, as the survival of a cancer cell depends by the relative presence of dependence receptors and their ligands.

Netrin-1 receptors (DCC and UNC5H) are the prototypes of dependence receptors. It is interesting to note that several papers show that during tumoral progression, resistance to dependence receptors-induced cell death could occur by an over-expression of netrin-1. Several studies performed in the lab have shown that interfering with the netrin-1 and its receptors interaction is sufficient to induce dependence receptor-dependent apoptosis and favour tumour regression. The netrin-1 inhibition strategy could be applied only in the fraction of tumours over-expressing netrin-1. Therefore, the knowledge of which cancer cells have selected this strategy to survive and what are the mechanisms involved in netrin-1 up-regulation in tumour cells could be important in developing personalized therapeutic treatments.

The aims of my project are: (i) to assess the role of netrin-1 and its receptors up-regulation in metastatic colorectal cancer. (ii) to test, in ex vivo model of primary colorectal tumour and in colorectal metastasis, the first humanized monoclonal antibody directed against netrin-1 (NP137), able to interfere with netrin-1/receptors interaction, in order to validate it as a new targeted therapy.

Summary of the project: The metastatic melanoma (MM) prognostic is in upheaval thanks to immunotherapies (ITs). But toxicities are important, the response rate is poor, their price is high and no response predictive factor has been approved so far. Dr Bonnefoy's team showed on mouses and patients that tumoral progression in MM was associated with a CD39 overexpression by the tumor infiltrating lymphocytes (TILs) and inhibition of this ectonucleosidase led to a cytotoxic TILs proliferation. Indeed CD39 transforms extracellular adenosine triphosphate into adenosine which has a strong immunosuppressive action. Also, they showed that a non-negligible subpopulation of TILs coexpressed CD39 and PD1 (a known immune check-point). Description of the project : The goal is to determine the response to ITs predictive value of the presence of CD39+ /PD1+ TILs in the tumoral microenvironnement of MM. A retrospective analyse of CD39 and PD1 expression will be conducted with immunohistochemistery on samples from patients suffering of MM treated by ITs since 2011. Simultaneously we will study by flow cytometry fresh tissue from cutaneous metastases of MM. The pro-inflammatory cytokines level of secretion by TILs will be compare to their CD39/PD1 expression. This level will also be analyzed after CD39's activity inhibition. Result: The retrospective approach will show the anatomic disposition of CD39 and PD1 expression within the tumor and his correlation or not with treatment response. Then the prospective analyze will permit to demonstrate that CD39 is an anergy marker of TILs and that its inhibition restore their functions. Thus, the CD39/PD1 coexpression by TILs could be a predictive factor of ITs response in MM

Summary of the project: NDifferentiation and proliferation index are two of the most prognostic features in pancreatic neuroendocrine tumors (PNET). It is unclear whether well-differentiated aggressive (grade 3 (G3)) tumours represent a separate entity or the end of the well-differentiated tumours spectrum. However, some patients have been described to progress from low G1/G2 to G3 tumours when they recur or metastasize. Molecular anomalies driving this progression are largely unknown. The aim of this project is to understand the molecular alterations involved in the progression of a subset of well-differentiated pancreatic neuroendocrine tumours toward aggressive neoplasms and to define a poor prognostic signature in well-differentiated low proliferating PNET. To address these questions, the evolution of the mutational load and the expression profile will be studied through exome sequencing and transcriptome analysis in 10 patients that evolved from low to high grade PNET with available tumor material at several time points. A poor prognosis signature will be derived by comparison with patients that had a low G1 PNET and never evolved during a 10 year follow up.

Title of the project: Patient-Derived Xenografts (PDXs) to study the mechanisms of resistance to sorafenib and to identify predictive markers of sorafenib response in patients with hepatocellular carcinoma

Place of the training course: Division of Liver Diseases, Department of Medicine,
Icahn School of Medicine at Mount Sinai, New York, New York, USA

Summary of the project: Liver cancer, ranks first among the tumors that have increased mortality in the last 20 years. Most patients are still diagnosed at advanced stages, where median survival is less than 1 year. In these patients, sorafenib is the only drug able to increase survival by an average of ~3 months, however in most of patients resistance develops after 5 months of treatment. Despite recent advancements in the molecular characterization of liver cancer, there are no validated predictive biomarkers of sorafenib resistance. This project aims to comprehensively evaluate the molecular mechanisms underlying sorafenib resistance in human liver cancer by using high-throughput molecular and genomic analysis and liver cancer patient-derived xenografts (PDX). PDX will be used to identify the driver mutations that confer growth advantage on the cancer cells when exposed to sorafenib. Afterwards, the presence of circulating markers of sorafenib resistance will be assessed in the bloodstream of liver cancer patients by analyzing circulating DNA and circulating tumor cells. This proposal will provide circulating tumor markers that could be easily used in the clinical setting to predict response to sorafenib. This will facilitate the implementation of target-oriented second line clinical trials. Our ultimate goal is to provide an innovative minimally invasive tool to improve decision-making in liver cancer patients.

Title of the project:PROGNOSTIC VALUE OF SINGLE-CELL RNA SEQUENCING IN HUMAN GLIOMAS

Place of the training course: Laboratory of Prof. Doron Merkler, Department of Pathology and Immunology, University of Geneva Medical School, and Service of Clinical Pathology, Geneva University Hospitals

Summary of the project: Résumé du projet de recherche: Recent advances in molecular pathology have broaden our knowledge about the biology of primary gliomas. Molecular classification has proven superior to the traditional histopathological diagnosis in predicting clinical outcomes and response to chemotherapy of gliomas. Therefore, in the WHO classification of brain tumors molecular analysis is becoming a crucial determinant in the final diagnosis together with histomorphological phenotyping. The growing number of clinically relevant genetic alterations urges genome-wide and transcriptomic analyses, where high-throughput RNA sequencing represents a highly sensitive and specific alternative. Moreover, this technique can further be combined with methodologies enabling the analysis of transcriptomes from individual cells. Single-cell RNA sequencing permits the cellular decomposition of complex tissues, such as gliomas, and is, therefore, ideally suited to investigate the extent and impact of intratumoral heterogeneity. The co-existence of tumoral subclones with different genetic mutations has been increasingly recognized as a crucial factor for treatment failure and recurrence. However, little is known about the direct prognostic relevance of intratumoral heterogeneity as determined by single-cell RNA sequencing. Here, we set out to implement a recently developed method for large-scale single-cell RNA sequencing in the Service of Clinical Pathology at the Geneva University Hospitals, in order to investigate genetic events in primary and secondary gliomas at the level of individual cells, and to find possible correlates of prognosis and recurrence.

Title of the project: A translational platform for the identification of novel targeted and personalized treatments of melanoma

Place of the training course: The Sahlgrenska Translational Melanoma Group,
Sahlgrenska Cancer Center, University of Gothenburg, Sweden

Summary of the project: Biomarkers of response to targeted therapies do not exist. The hypothesis of this project is that the response of the patient's tumor itself could constitute the biomarker. Jonas Nilsson's team has developed a melanoma platform of pharmaco-genetically characterized patient-derived mouse xenograft models (PDXes) to devise unbiased and new therapeutic strategies against melanoma. Tumor material from patients with metastatic melanoma stage III and stage IV is extensively used to generate models and to gain genetic information to predict treatment responses. The first aim of the project is to use the PDX platform to guide the right patient to the right clinical trial. Since the patient-like mouse models do not have an immune system, the second aim of the project is to develop and use genetically-engineered mouse models of melanoma to test the effect of new target and immune therapies.

Summary of the project: Low grade gliomas are the most common brain tumors in children causing pharmacoresistant epilepsy, particularly the mixed glio-neuronal tumor subtypes. Only a minority of them are evolutive and the most common causes of morbidity are due to epilepsy, adjuvant treatment and progression of residual tumor. We focus our integrative work on dysembryoplastic neuroepithelial tumors (DNTs) first described at Sainte-Anne hospital and for which we have a large annotated data base . Until now, the rarity and the scarcity of tissue available for histomolecular and genetic analyses have hampered the identification of specific alterations in this entity. We will study a series of 60 DNTs including progressive forms. The aim is to analyze and understand the molecular profiles of different types of tumors in order to refine their classification and therapeutic management. A first step will be the analysis of tumor methylation profiles and sequencing. In a second set of experiments (gene set enrichment anlaysis, RNAseq single cell...) we plan to confirm the specific abnormalities and then to validate by in situ tests in order to develop tools for routine diagnostic practice

Title of the project: Study of a novel endothelial regulator as a potential anti-angiogenic target

Place of the training course: Department of Fundamental Oncology, UNIL-CHUV

Summary of the project: Cancer burden in industrialized countries is increasing due to aging of the population. In
addition to the improvement of preventive and diagnostic methods, there is still a need for the
development of novel effective therapies. Tumor growth and metastasis are dependent on the
formation of new blood vessels, therefore targeting the tumor vasculature represents one of the
possible strategies. Until now, anti-angiogenic therapies have focused on the destruction of the
tumor vasculature by inhibiting the vascular endothelial growth factor (VEGF) pathway. However,
anti-VEGF drugs show only limited benefit in patients, highlighting the need for alternative
approaches for targeting tumor vasculature and better understanding the mechanisms of tumor
angiogenesis. The host laboratory has recently identified a new endothelial cell-specific membrane
protein involved in vessel formation. The aims of my project are: (i) to analyze its expression in
human tumor samples, (ii) to investigate its function in tumor angiogenesis using new genetic
models and (iii) to characterize its action at the cellular and molecular levels. These studies will
provide new knowledge about the mechanisms involved in physiological and pathological
angiogenesis. Our findings will allow us to assess the therapeutical potential of this new target.